diff jbrowsehubToApollo.xml @ 0:ce4f91831680 draft default tip

planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 5367a00befb467f162d1870edb91f9face72e894

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jbrowsehubToApollo.xml	Fri Feb 16 10:57:13 2018 -0500
@@ -0,0 +1,110 @@
+<tool id="jbrowsehubtoapollo" name="JBrowseHub To Apollo" version="1.0.0">
+    <description>
+        This Galaxy tool is used to prepare your files to be ready for displaying on Apollo
+    </description>
+
+    <requirements>
+        <requirement type="package" version="3.0.3">apollo_api</requirement>
+    </requirements>
+
+    <stdio>
+    </stdio>
+
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p $output.extra_files_path;
+        ## Dump the tool parameters into a JSON file 
+        python $json_file parameters.json;
+        python $__tool_directory__/jbrowsehubToApollo.py --data_json parameters.json -o $output
+    ]]></command>
+    <configfiles>
+        <configfile name="json_file">
+import json
+import sys
+
+file_path = sys.argv[1]
+#set global data_parameter_dict = {}
+#silent $data_parameter_dict.update({"action": str($action)})
+#silent $data_parameter_dict.update({"action": str($action)})
+#silent $data_parameter_dict.update({"species_name": str($species_name)})
+#set apollo_admin = {"user_email": str($admin_username), "password": str($admin_password)}
+#silent $data_parameter_dict.update({"apollo_admin": $apollo_admin})
+#silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
+#silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)})
+#slient $data_parameter_dict.update({"jbrowse_hub": str($jbrowse_hub.extra_files_path)})
+#silent $data_parameter_dict.update({"port": str($advanced_options.port)})
+#silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
+with open(file_path, 'w') as f:
+    json.dump($data_parameter_dict, f)
+        </configfile>
+    </configfiles>
+
+
+    <inputs>
+        <param 
+                format="jbrowsehub" 
+                type="data"
+                name="jbrowse_hub" 
+                label="JBrowse Hub created by JBrowse Archive Creator" 
+        />
+
+        <param name="action" type="select" label="Choose to create a new organism or overwrite an organism">
+            <option value="add" selected="true">Add a new organism to Apollo</option>
+            <option value="overwrite">Overwrite an existing organism on Apollo</option>
+        </param>
+        
+        <param
+                name="species_name"
+                type="text"
+                size="30"
+                value="unknown"
+                label="Species name"
+        />
+
+        <param name="admin_username" type="text" label="Admin username" help="Login in with Apollo admin account">
+            <sanitizer>
+                <valid initial="string.letters,string.digits">
+                    <add value="@-=_.()/+*^,:?!"/>
+                </valid>
+            </sanitizer>
+        </param>
+
+        <param
+            name="admin_password"
+            type="text"
+            label="Admin password"
+        />
+
+        <conditional name="advanced_options">
+            <param name="advanced_options_selector" type="select" label="Advanced options">
+                <option value="off" selected="true">Hide advanced options</option>
+                <option value="on">Display advanced options</option>
+            </param>
+            <!-- TODO: Avoid redundancy here -->
+            <when value="on">
+                <param name="port" type="integer" min="8000" max="8888" value="8080" label="Port number of Apollo" />
+                <param name="debug_mode" type="select" label="Activate debug mode"> 
+                    <option value="false" selected="true">No</option>
+                    <option value="true">Yes</option>
+                    <help>
+                        Use this option if you are a G-OnRamp developer
+                    </help>
+                </param>
+            </when>
+            <when value="off">
+                <param name="port" type="hidden" value="8080" />
+                <param name="debug_mode" type="hidden"
+                       value="false">
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="html" name="output" label="${tool.name}" />
+    </outputs>
+
+    <help>
+        This Galaxy tool is used to create or overwrite an organism on an Apollo server with a jbrowse hub created by JBrowse Archive Creator. 
+    </help>
+    <citations>
+    </citations>
+</tool>
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